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Structural basis for differential recognition of tyrosine phosphorylated sites in the linker for activation of T cells (lat) by the adaptor protein gads
Analyse Structural basis for differential recognition of tyrosine phosphorylated sites… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R1P
- Type
- protein
- Length
- 414 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GRB2-related adaptor protein 2; Lat PY171 peptide
- UniProt
- O89100
- Ligands
- ACE, SO4
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | GRB2-related adaptor protein 2 | protein | 95 | 18% helix, 25% strand | O89100 |
| B, C | GRB2-related adaptor protein 2 | protein | 100 | 19% helix, 24% strand | O89100 |
| E, F, G, H | Lat PY171 peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains E, B, F, G, C, H
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.60 | 0.81 | 38 | empty |
| 2 | 89 | 0.45 | 0.80 | 17 | empty |
| 3 | 92 | 0.43 | 0.79 | 16 | empty |
| 4 | 68 | 0.41 | 0.81 | 14 | empty |
| 5 | 77 | 0.34 | 0.75 | 18 | empty |
Interfaces
11 interfaces between chains.
- A–B · 891 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 831 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 713 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 526 Ų buried · 2 hydrogen bonds · protein-protein
- D–G · 468 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, phosphorylation).
Compared structures
- 1R1P · Structural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the… · the same entry in another collection · chain H against H, TM-score 1.00
- O89100 · AlphaFold monomer V2.0 prediction for GRB2-related adaptor protein 2 (O89100) · a predicted model of the same protein · chain B against A, TM-score 0.93
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O89100
- Elsewhere: RCSB PDB 1R1P · PDBe 1R1P · UniProt O89100
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